User:Eric Martz/Molecular Playground/Authoring: Difference between revisions

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 ==Designing An Effective Module==
-'''Use light colors on a black background.''' Because MP projects in a well lit atrium, generally a black background (which will appear medium gray) works best. Dark colors are hard to see on the black background, so use light colors as much as possible. In particular, Jmol's default [[CPK]] colors for carbon, oxygen and nitrogen are marginally visible. Therefore the support script provided for MP includes a function ''colorAllLightCPK'' that applies lighter colors to these elements.
+===Use light colors on a black background===
-'''Permit rotation by onlookers.''' MP invites onlookers to interact by rotating the structure at any time. Therefore, scripts should be designed to permit rotation as much as possible. Furthermore, it may be desirable for the user-set orientation to remain while the script proceeds, perhaps all the way to the end of the script. For example, a ''moveto'' command precludes rotation until the specified orientation is completed. In the version of Jmol currently used in Proteopedia (11.8.9 in December, 2009), ''zoomto'' commands also enforce the current orientation, "fighting" with the onlooker who attempts rotation during the timed zoomto. Therefore, the support script provided for MP includes a function ''zoomRotatableTo()'' that performs the zoom while permitting rotation.
+Because MP projects in a well lit atrium, generally a black background (which will appear medium gray) works best. Dark colors are hard to see on the black background, so use light colors as much as possible. In particular, Jmol's default [[CPK]] colors for carbon, oxygen and nitrogen are marginally visible. Therefore the support script provided for MP includes a function ''colorAllLightCPK'' that applies lighter colors to these elements.
+===Facilitate rotation by onlookers===
+MP invites onlookers to interact by rotating the structure at any time. Therefore, scripts should be designed to permit rotation as much as possible. Furthermore, it may be desirable for the user-set orientation to remain while the script proceeds, perhaps all the way to the end of the script. For example, a ''moveto'' command precludes rotation until the specified orientation is completed. In the version of Jmol currently used in Proteopedia (11.8.9 in December, 2009), ''zoomto'' commands also enforce the current orientation, "fighting" with the onlooker who attempts rotation during the timed zoomto. Therefore, the support script provided for MP includes a function ''zoomRotatableTo()'' that performs the zoom while permitting rotation.
+===Avoid displays that seriously slow Jmol===
+The following displays cause spinning or rotation to become slow and jerky in the full-sized (1024 x 768 pixels) MP projection. Your displays will be more satisfying if these can be avoided. A good way to test this is to try your scripts in the Jmol application at 1024 x 768 pixels.
+* '''Large numbers of spacefilled atoms''', such as spacefilling all atoms in a protein. The higher the zoom, the jerkier the spinning.
+* '''Translucency'''.
+* '''High-Quality Display''', namely ''set antialiasdisplay true''. The MPSupportVersion01.spt actually uses high-quality when the script is displayed in the applet, because at the typical applet size (450 x 350 pixels) the speed penalty is acceptable.
+* '''Trace''' is slower than backbone. Thick traces are slower than thin traces. High zoom levels are even slower. You can get away with a thin trace at low zoom for a moderate-sized protein.
 ==Jmol Scripting Options==
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 Your MP web page need not be in Proteopedia. You can put it on another server, and it can be linked to the name of your module at [[http://molecularplayground.org Molecular Playground]].
-==Displays to Avoid==
-The following displays cause spinning or rotation to become slow and jerky in the full-sized (1024 x 768 pixels) MP projection. Your displays will be more satisfying if these can be avoided. A good way to test this is to try your scripts in the Jmol application at 1024 x 768 pixels.
-* '''Large numbers of spacefilled atoms''', such as spacefilling all atoms in a protein. The higher the zoom, the jerkier the spinning.
-* '''Translucency'''.
-* '''High-Quality Display''', namely ''set antialiasdisplay true''. The MPSupportVersion01.spt actually uses high-quality when the script is displayed in the applet, because at the typical applet size (450 x 350 pixels) the speed penalty is acceptable.
-* '''Trace''' is slower than backbone. Thick traces are slower than thin traces. High zoom levels are even slower. You can get away with a thin trace at low zoom for a moderate-sized protein.
 ==Dimensions of Projected Jmol==